remove old datamodel javadoc
[jabaws.git] / website / full_javadoc / compbio / data / sequence / class-use / Alignment.html
index af197d7..ac64d26 100644 (file)
@@ -2,12 +2,12 @@
 <!--NewPage-->\r
 <HTML>\r
 <HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
+<!-- Generated by javadoc (build 1.6.0_24) on Fri Aug 12 14:32:36 BST 2011 -->\r
 <TITLE>\r
 Uses of Class compbio.data.sequence.Alignment\r
 </TITLE>\r
 \r
-<META NAME="date" CONTENT="2010-02-17">\r
+<META NAME="date" CONTENT="2011-08-12">\r
 \r
 <LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
 \r
@@ -91,7 +91,7 @@ Packages that use <A HREF="../../../../compbio/data/sequence/Alignment.html" tit
 </TR>\r
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD><A HREF="#compbio.data.msa"><B>compbio.data.msa</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
+<TD>Web Service interfaces for JAva Bioinformatics Analysis Web Services.&nbsp;</TD>\r
 </TR>\r
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD><A HREF="#compbio.data.msa.jaxws"><B>compbio.data.msa.jaxws</B></A></TD>\r
@@ -99,8 +99,8 @@ Packages that use <A HREF="../../../../compbio/data/sequence/Alignment.html" tit
 </TR>\r
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD><A HREF="#compbio.data.sequence"><B>compbio.data.sequence</B></A></TD>\r
-<TD>A data model for multiple sequence alignment web services 
- Classes in this package have no dependencies to other sources in the project.&nbsp;</TD>\r
+<TD>A data model for multiple sequence alignment web services and utility methods
+ that work on the objects of this model.&nbsp;</TD>\r
 </TR>\r
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD><A HREF="#compbio.runner"><B>compbio.runner</B></A></TD>\r
@@ -134,7 +134,7 @@ Uses of <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 <CODE>&nbsp;<A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B>MsaWS.</B><B><A HREF="../../../../compbio/data/msa/MsaWS.html#getResult(java.lang.String)">getResult</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
+<TD><CODE><B>MsaWS.</B><B><A HREF="../../../../compbio/data/msa/MsaWS.html#getResult(java.lang.String)">getResult</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;jobId)</CODE>\r
 \r
 <BR>\r
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Return the result of the job.</TD>\r
@@ -200,7 +200,7 @@ Uses of <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 <CODE>static&nbsp;<A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B>ClustalAlignmentUtil.</B><B><A HREF="../../../../compbio/data/sequence/ClustalAlignmentUtil.html#readClustalFile(java.io.File)">readClustalFile</A></B>(java.io.File&nbsp;file)</CODE>\r
+<TD><CODE><B>ClustalAlignmentUtil.</B><B><A HREF="../../../../compbio/data/sequence/ClustalAlignmentUtil.html#readClustalFile(java.io.File)">readClustalFile</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/File.html?is-external=true" title="class or interface in java.io">File</A>&nbsp;file)</CODE>\r
 \r
 <BR>\r
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
@@ -208,7 +208,7 @@ Uses of <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 <CODE>static&nbsp;<A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B>ClustalAlignmentUtil.</B><B><A HREF="../../../../compbio/data/sequence/ClustalAlignmentUtil.html#readClustalFile(java.io.InputStream)">readClustalFile</A></B>(java.io.InputStream&nbsp;instream)</CODE>\r
+<TD><CODE><B>ClustalAlignmentUtil.</B><B><A HREF="../../../../compbio/data/sequence/ClustalAlignmentUtil.html#readClustalFile(java.io.InputStream)">readClustalFile</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/InputStream.html?is-external=true" title="class or interface in java.io">InputStream</A>&nbsp;instream)</CODE>\r
 \r
 <BR>\r
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Read Clustal formatted alignment.</TD>\r
@@ -224,7 +224,7 @@ Uses of <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 <CODE>static&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B>ClustalAlignmentUtil.</B><B><A HREF="../../../../compbio/data/sequence/ClustalAlignmentUtil.html#writeClustalAlignment(java.io.OutputStream, compbio.data.sequence.Alignment)">writeClustalAlignment</A></B>(java.io.OutputStream&nbsp;outStream,\r
+<TD><CODE><B>ClustalAlignmentUtil.</B><B><A HREF="../../../../compbio/data/sequence/ClustalAlignmentUtil.html#writeClustalAlignment(java.io.Writer, compbio.data.sequence.Alignment)">writeClustalAlignment</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/Writer.html?is-external=true" title="class or interface in java.io">Writer</A>&nbsp;out,\r
                       <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>&nbsp;alignment)</CODE>\r
 \r
 <BR>\r
@@ -251,8 +251,8 @@ Uses of <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 <CODE>static&nbsp;<A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B>Util.</B><B><A HREF="../../../../compbio/runner/Util.html#readClustalFile(java.lang.String, java.lang.String)">readClustalFile</A></B>(java.lang.String&nbsp;workDirectory,\r
-                java.lang.String&nbsp;clustFile)</CODE>\r
+<TD><CODE><B>Util.</B><B><A HREF="../../../../compbio/runner/Util.html#readClustalFile(java.lang.String, java.lang.String)">readClustalFile</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;workDirectory,\r
+                <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;clustFile)</CODE>\r
 \r
 <BR>\r
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
@@ -277,7 +277,7 @@ Uses of <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 <CODE>&nbsp;<A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B>Tcoffee.</B><B><A HREF="../../../../compbio/runner/msa/Tcoffee.html#getResults(java.lang.String)">getResults</A></B>(java.lang.String&nbsp;workDirectory)</CODE>\r
+<TD><CODE><B>Mafft.</B><B><A HREF="../../../../compbio/runner/msa/Mafft.html#getResults(java.lang.String)">getResults</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;workDirectory)</CODE>\r
 \r
 <BR>\r
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
@@ -285,7 +285,7 @@ Uses of <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 <CODE>&nbsp;<A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B>ClustalW.</B><B><A HREF="../../../../compbio/runner/msa/ClustalW.html#getResults(java.lang.String)">getResults</A></B>(java.lang.String&nbsp;workDirectory)</CODE>\r
+<TD><CODE><B>ClustalW.</B><B><A HREF="../../../../compbio/runner/msa/ClustalW.html#getResults(java.lang.String)">getResults</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;workDirectory)</CODE>\r
 \r
 <BR>\r
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
@@ -293,7 +293,7 @@ Uses of <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 <CODE>&nbsp;<A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B>Probcons.</B><B><A HREF="../../../../compbio/runner/msa/Probcons.html#getResults(java.lang.String)">getResults</A></B>(java.lang.String&nbsp;workDirectory)</CODE>\r
+<TD><CODE><B>Tcoffee.</B><B><A HREF="../../../../compbio/runner/msa/Tcoffee.html#getResults(java.lang.String)">getResults</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;workDirectory)</CODE>\r
 \r
 <BR>\r
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
@@ -301,7 +301,7 @@ Uses of <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 <CODE>&nbsp;<A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B>Muscle.</B><B><A HREF="../../../../compbio/runner/msa/Muscle.html#getResults(java.lang.String)">getResults</A></B>(java.lang.String&nbsp;workDirectory)</CODE>\r
+<TD><CODE><B>Muscle.</B><B><A HREF="../../../../compbio/runner/msa/Muscle.html#getResults(java.lang.String)">getResults</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;workDirectory)</CODE>\r
 \r
 <BR>\r
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
@@ -309,7 +309,15 @@ Uses of <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 <CODE>&nbsp;<A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B>Mafft.</B><B><A HREF="../../../../compbio/runner/msa/Mafft.html#getResults(java.lang.String)">getResults</A></B>(java.lang.String&nbsp;workDirectory)</CODE>\r
+<TD><CODE><B>ClustalO.</B><B><A HREF="../../../../compbio/runner/msa/ClustalO.html#getResults(java.lang.String)">getResults</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;workDirectory)</CODE>\r
+\r
+<BR>\r
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>&nbsp;<A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
+<TD><CODE><B>Probcons.</B><B><A HREF="../../../../compbio/runner/msa/Probcons.html#getResults(java.lang.String)">getResults</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;workDirectory)</CODE>\r
 \r
 <BR>\r
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
@@ -334,7 +342,23 @@ Uses of <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 <CODE>&nbsp;<A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B>TcoffeeWS.</B><B><A HREF="../../../../compbio/ws/server/TcoffeeWS.html#getResult(java.lang.String)">getResult</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
+<TD><CODE><B>ClustalWS.</B><B><A HREF="../../../../compbio/ws/server/ClustalWS.html#getResult(java.lang.String)">getResult</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;jobId)</CODE>\r
+\r
+<BR>\r
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>&nbsp;<A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
+<TD><CODE><B>_MsaService.</B><B><A HREF="../../../../compbio/ws/server/_MsaService.html#getResult(java.lang.String)">getResult</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;jobId)</CODE>\r
+\r
+<BR>\r
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>&nbsp;<A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
+<TD><CODE><B>MuscleWS.</B><B><A HREF="../../../../compbio/ws/server/MuscleWS.html#getResult(java.lang.String)">getResult</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;jobId)</CODE>\r
 \r
 <BR>\r
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
@@ -342,7 +366,7 @@ Uses of <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 <CODE>&nbsp;<A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B>ProbconsWS.</B><B><A HREF="../../../../compbio/ws/server/ProbconsWS.html#getResult(java.lang.String)">getResult</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
+<TD><CODE><B>MafftWS.</B><B><A HREF="../../../../compbio/ws/server/MafftWS.html#getResult(java.lang.String)">getResult</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;jobId)</CODE>\r
 \r
 <BR>\r
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
@@ -350,7 +374,7 @@ Uses of <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 <CODE>&nbsp;<A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B>MuscleWS.</B><B><A HREF="../../../../compbio/ws/server/MuscleWS.html#getResult(java.lang.String)">getResult</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
+<TD><CODE><B>TcoffeeWS.</B><B><A HREF="../../../../compbio/ws/server/TcoffeeWS.html#getResult(java.lang.String)">getResult</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;jobId)</CODE>\r
 \r
 <BR>\r
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
@@ -358,7 +382,7 @@ Uses of <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 <CODE>&nbsp;<A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B>MafftWS.</B><B><A HREF="../../../../compbio/ws/server/MafftWS.html#getResult(java.lang.String)">getResult</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
+<TD><CODE><B>ProbconsWS.</B><B><A HREF="../../../../compbio/ws/server/ProbconsWS.html#getResult(java.lang.String)">getResult</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;jobId)</CODE>\r
 \r
 <BR>\r
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
@@ -366,7 +390,7 @@ Uses of <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 <CODE>&nbsp;<A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B>ClustalWS.</B><B><A HREF="../../../../compbio/ws/server/ClustalWS.html#getResult(java.lang.String)">getResult</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
+<TD><CODE><B>ClustalOWS.</B><B><A HREF="../../../../compbio/ws/server/ClustalOWS.html#getResult(java.lang.String)">getResult</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;jobId)</CODE>\r
 \r
 <BR>\r
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r